[Bioc-devel] Reference manual as HTML

[Laurent Gatto]

My experience with pkgdown is very positive. As mentioned by Stuart, I use travis to automatically build the webpage after a successful check and serve it as a gh-page.

I find it particularly useful as it displays the devel version of the vignettes and individual manual pages, which often come handy to answer questions related to new features or bug fixes and to add a link to the relevant manual page (rather than a large pdf) or vignette section. The webpage is also a good starting point to learn about new packages, as all the documentation sources, README, vignettes and individual man pages (which can easily be overwhelming for large packages) are readily available to read and search.

Laurent

________________________________________
From: Martin Morgan <mtmorgan.bioc using gmail.com>
Sent: 25 September 2019 23:10
To: Laurent Gatto; Ludwig Geistlinger; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Reference manual as HTML

Our recollection is that there is no 'flag' in R CMD build to create HTML rather than PDF vignettes; without that it would be non-trivial to create html output, e.g., links across pages. (I *think* the installed package html help pages are generated on the fly...)

What is your experience with pkgdown?

Martin

On 9/25/19, 9:44 AM, "Bioc-devel on behalf of Laurent Gatto" <bioc-devel-bounces using r-project.org on behalf of laurent.gatto using uclouvain.be> wrote:

    I think this would be very useful. This is one of the reasons I create pkgdown sites for my packages: manual pages, news and html vignettes are readily available for all (including me) to browse.

    Best wishes,

    Laurent

    ________________________________________
    From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ludwig Geistlinger <Ludwig.Geistlinger using sph.cuny.edu>
    Sent: 25 September 2019 13:31
    To: bioc-devel using r-project.org
    Subject: [Bioc-devel] Reference manual as HTML

    Dear Bioc-Team,


    I repeatedly wondered whether it would be possible to display the reference manual
    as HTML instead of PDF on a package's landing page. This is already possible for vignettes.

    HTML reference manuals have at least two advantages:

    1. links to functions of other package in the man pages of my package would
    actually work. Links to functions / classes of other packages of the form

    \code{\link{p.adjust}}

    or

    \code{\linkS4class{SummarizedExperiment}}

    within the pdf reference manual currently point nowhere (bring me back to the
    first page of the pdf). Within the html reference manual

    help(package="myPackage", help_type="html")

    these links work as expected, ie bring me to the help pages of functions / classes
    of other packages.

    2. I could easily refer users to the documentation link of a specific function
    (without them having to search through the pdf) such as "check the documentation of
    the DESeq function here: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fbioc%2FDESeq2%2Fman%2FDESeq.html&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ce38d0811b2c94f5450f808d741fcc9a6%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637050426278839970&sdata=hEk11QlPbH1cNC1xvidpDjKtdU9lqrkxBdvK0u2qYxM%3D&reserved=0".

    (where the link would be preferably: bioconductor.org/packages/DESeq2/man/DESeq.html).


    Thank you,

    Ludwig

            [[alternative HTML version deleted]]

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